Identification and validation of a novel cellular senescence-related lncRNA prognostic signature for predicting immunotherapy response in stomach adenocarcinoma

Predicting immune status and gene mutations in stomach adenocarcinoma patients based on inflammatory response-related prognostic features

BACKGROUND

Stomach adenocarcinoma (STAD) is an aggressive malignant tumor. Herein, we characterized the prognosis based on inflammatory response-related features and evaluated their potential impact on survival and immune status of STAD patients.

METHODS

Inflammation-related genes obtained from public databases were used to analyze the inflammatory response scores of STAD samples. The differentially expressed genes (DEGs) between STAD and adjacent gastric tissue were then analyzed using the "limma" package. Genes associated with STAD prognosis were obtained from the intersection of inflammation-related genes and DEGs. The key genes screened by last absolute shrinkage and selection operator (LASSO) Cox and stepwise regression analyses were used to construct prognostic models and nomograms. The tumor immune dysfunction exclusion (TIDE) algorithm was used to assess potential differences in immunotherapy response between high- and low-risk groups and to explore gene mutation signatures using the R software maftools package. In addition, GSEA was used to predict pathway characteristics between different subgroups. Finally, scratch and transwell assays were performed to explore the role of SERPINE1 in STAD cells.

RESULTS

We found that a high-inflammatory group was associated with poor prognosis in STAD patients. 14 inflammation-related DEGs out of 126 DEGs were identified to be associated with the prognosis of STAD patients, and the prognostic models and nomograms constructed from the subsequently identified key genes (SLC7A1, CD82, SERPINE1 ROS1 and SLC7A2) demonstrated a good predictive performance in terms of prognosis of STAD. Patients in the STAD high-risk group had higher StromalScore and TIDE scores. It was also found that patients in the STAD low-risk group may have a higher mutation burden. Enrichment analysis revealed significant enrichment of epithelial-mesenchymal transition, angiogenesis and KRAS pathways in the high-risk group. In-vitro experiments showed that down-regulation of SERPINE1 attenuated the migratory and invasive abilities of AGS cells.

CONCLUSION

This study provides new insights into prognostic prediction and immunotherapy for STAD from the perspective of the inflammatory response.

Molecular signatures of cellular senescence in cancer: a critical review of prognostic implications and therapeutic opportunities

Cellular senescence is a state of permanent loss of proliferative capacity. Therefore, cells that reach a senescent state prevent tumor initiation, acting as an anti-tumor mechanism. However, despite not being proliferative, senescent cells have high secretory activity, constituting the Senescence-Associated Secretory Phenotype (SASP). SASP includes thousands of soluble molecules and extracellular vesicles, through which senescent cells can affect other cells and the extracellular matrix. In advanced tumors, the enrichment of senescent cells can have anti- or pro-tumor effects depending on features like SASP composition, tumor microenvironment (TME) composition, the anatomic site, histopathologic characteristics of malignancy, and tumor molecular background. We reviewed the studies assessing the impact of the senescence status, measured by mRNA or lncRNA molecular signatures, in the prognosis and other clinically relevant information in cancer, including anti-tumor immunity and response to therapy. We discussed the pros and cons of different strategies to define those molecular signatures and the main limitations of the studies. Finally, we also raised clinical challenges regarding the crossroad between cellular senescence and cancer prognosis, including some therapeutic opportunities in the field.

Integrated bulk and single-cell transcriptomic analysis unveiled a novel cuproptosis-related lipid metabolism gene molecular pattern and a risk index for predicting prognosis and antitumor drug sensitivity in breast cancer

Breast cancer is the second most prevalent malignant tumor worldwide and is highly heterogeneous. Cuproptosis, a newly identified form of cell death, is intimately connected to lipid metabolism. This study investigated breast cancer heterogeneity through the lens of cuproptosis-related lipid metabolism genes (CLMGs), with the goal of predicting patient prognosis, immunotherapy efficacy, and sensitivity to anticancer drugs. By utilizing transcriptomic data from The Cancer Genome Atlas (TCGA) for breast cancer, we identified 682 CLMGs and applied the nonnegative matrix factorization (NMF) method to categorize breast cancer patients into four distinct clusters: cluster 1, ''immune-cold and stroma-poor''; cluster 2, ''immune-infiltrated''; cluster 3, ''stroma-rich''; and cluster 4, ''moderate infiltration''. We subsequently developed a risk model based on CLMGs that incorporates ACSL1, ATP2B4, ATP7B, ENPP6, HSPH1, PIP4K2C, SRD5A3, and ULBP1. This model demonstrated excellent prognostic predictive performance in both the internal (testing and entire sets) and external (GSE20685 and Kaplan-Meier Plotter sets) validation sets. High-risk patients presented lower expression levels of immune checkpoint-related genes and lower immunophenoscores (IPSs), whereas low-risk patients presented higher CD8+ T-cell infiltration levels and IPSs. Furthermore, the risk index was positively correlated with tumor cell stemness and could predict sensitivity to anticancer drugs. We also confirmed that SRD5A3 was highly expressed in breast cancer and participated in promoting the proliferation and migration of breast cancer cells. In conclusion, the results of this study provide new insights and strategies for assessing prognosis and implementing precision treatment for breast cancer through the lens of CLMGs.

AC129507.1 is a ferroptosis-related target identified by a novel mitochondria-related lncRNA signature that is involved in the tumor immune microenvironment in gastric cancer

BACKGROUND

Gastric cancer (GC) is one of the most common malignancies. Previous studies have shown that mitochondrial metabolism is associated with malignancies. However, relevant research on mitochondria-related lncRNAs in GC is lacking.

METHODS

We integrated the corresponding information of patients with GC from The Cancer Genome Atlas (TCGA) database. Mitochondria-related lncRNAs were selected based on differential expression and a correlation analysis to construct a prognostic model. The mutation data were analyzed to distinguish differences in the tumor mutation burden (TMB). Single-sample gene set enrichment analysis (ssGSEA) was performed to evaluate immunological differences. A series of cell-based experiments were adopted to evaluate the biological behavior of GC.

RESULTS

A total of 1571 mitochondria-related lncRNAs were identified. A prognostic signature incorporating nine lncRNAs was built based on 293 suitable GC cases and could predict patient prognosis. The TMB and ssGSEA indicated that the low-risk group displayed increased immune function. The enrichment analysis indicated that the differentially expressed genes were enriched in metabolic functions. AC129507.1 was significantly upregulated in GC cells and associated with a poor prognosis, and its knockdown inhibited the proliferation and migration of GC cells. Mechanistically, silencing AC129507.1 led to abnormal glycolipid metabolism and oxidative stress, thus inducing ferroptosis.

CONCLUSIONS

Our nine-lncRNA risk signature could powerfully predict patient prognosis. AC129507.1 promoted the malignant phenotypes of GC cells. AC129507.1 could play a nonnegligible role in GC by promoting the formation of a immunosuppressive tumor microenvironment by inhibiting the initiation of ferroptosis, which needs to be further explored.

Training and experimental validation a novel anoikis- and epithelial‒mesenchymal transition-related signature for evaluating prognosis and predicting immunotherapy efficacy in gastric cancer

Anoikis resistance and improper activation of epithelial‒mesenchymal transition (EMT) are critical factors in tumor metastasis and progression. Despite their interaction, the combined impact of anoikis and EMT on prognosis and immunotherapy in gastric cancer remains underexplored. In this study, we identified 354 anoikis- and EMT-related genes (AERGs) through Venn analysis and performed unsupervised clustering to classify gastric cancer patients into two molecular clusters: A and B. Molecular cluster A showed poor prognosis and an immunosuppressive tumor microenvironment, suggesting a "cold tumor" phenotype. Then, a novel AERG-related prognostic model comprising CD24, CRYAB, MMP11, MUC4, PRKAA2, SERPINE1, SKP2, and TP53 was constructed and validated, accurately predicting the 1-, 3-, and 5-year survival rates of gastric cancer patients. Multivariate analysis revealed that the AERG-related risk score was an independent prognostic factor (hazard ratio = 1.651, 95% confidence interval = 1.429-1.907, P<0.001). Further studies demonstrated that, compared to the high-risk group, the low-risk group exhibited higher CD8+ T cell infiltration, tumor mutational burden, immunophenoscores, and lower tumor immune dysfunction and exclusion scores, indicating potential sensitivity to immunotherapy. RT‒qPCR and immunohistochemical staining validated the expression levels of the model's molecular markers. Overall, our AERG-related model shows promise for predicting outcomes and guiding the selection of tailored and precise therapies for gastric cancer patients.

Non-coding RNAs participate in interactions between senescence and gastrointestinal cancers

Relationships between cellular senescence and gastrointestinal cancers have gained prominence in recent years. The currently accepted theory suggests that cellular senescence and cancer occurrence exhibit "double-edged sword" effects. Cellular senescence is related to cancer via four "meta-hallmarks" i.e., genomic instability, epigenetic alterations, chronic inflammation, and dysbiosis, along with two "antagonistic hallmarks" i.e., telomere attrition and stem cell exhaustion. These relationships are characterized by both agonistic and antagonistic elements, but the existence of an intricate dynamic balance remains unknown. Non-coding RNAs (ncRNAs) have vital roles in post-transcriptional regulation, but how they participate in agonistic and antagonistic relationships between cellular senescence and gastrointestinal cancers remains to be fully investigated. In this article, we systematically review how ncRNAs (including microRNAs (miRNAs), long ncRNAs (lncRNAs), and circularRNAs (circRNAs)) participate in interactions between cellular senescence and gastrointestinal cancers. Our aim is to elucidate a triangular relationship between "ncRNAs-senescence-gastrointestinal cancers" which considered these three elements as an equal important standing. We are keen to identify prognostic or therapeutic targets for gastrointestinal cancers from, i.e., aging-related ncRNAs, or discover novel strategies to treat and manage in the elderly. We seek to clarify complex relationships where ncRNAs participate in "senescence-gastrointestinal cancers" interactions.

A New Cuproptosis-Related lncRNAs Model for Predicting the Prognosis of Hepatitis B Virus-Associated Hepatocellular Carcinoma and Experimental Validation of LINC01269

Background

Hepatocellular carcinoma (HCC) triggered by Hepatitis B virus (HBV) remains a significant clinical challenge, necessitating novel therapeutic interventions. Copper ionophores, recognized for introducing an innovative type of programmed cell death termed cuproptosis, present promising potentials for cancer therapy. Nevertheless, The role of cuproptosis-related lncRNAs (CRLRs) in HBV-HCC has not been clearly elucidated.

Methods

This study utilised univariate Cox, least absolute shrinkage and selection operator (LASSO), and multivariable Cox regression analyses to establish a signature for CRLRs in HBV-HCC. This prognostic model was validated with an independent internal validation cohort, combined with clinical parameters, and used to construct a nomogram for patient survival predictions. Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) were employed to explore associated biological pathways. Additionally, a protein-protein interaction (PPI) network was developed, and implications for tumour mutational burden (TMB) and drug response were examined. A comprehensive bioinformatics analysis of these hub CRLRs was performed, followed by experimental validation through quantitative real-time PCR (qRT-PCR) and functional cellular assays.

Results

The nomogram showed high predictive accuracy for HBV-HCC patient survival. GO and GSEA analyses indicated that these lncRNAs are involved in pathways related to cancer and oestrogen metabolism. A PPI network consisting of 201 nodes and 568 edges was developed, and the TMB and drug response differed significantly between high- and low-risk groups. Analyses identified three hub CRLRs, SOS1-IT1, AC104695.3, and LINC01269, which were significantly differentially expressed in HCC tissues. In vitro, LINC01269 was found to enhance HCC cell proliferation, invasion, and migration.

Conclusion

The first systematic exploration of the roles of CRLRs in HBV-HCC demonstrates their critical involvement in the disease's pathogenesis and possible therapeutic implication. The distinct expression patterns and significant biological pathways suggest that these lncRNAs may facilitate novel therapeutic targets.

Identification of anoikis-related molecular patterns and the novel risk model to predict prognosis, tumor microenvironment infiltration and immunotherapy response in bladder cancer

Background

Anoikis, a unique form of cell death, serves as a vital part of the organism's defense by preventing shedding cells from re-attaching to the incorrect positions, and plays pivotal role in cancer metastasis. Nonetheless, the specific mechanisms among anoikis, the clinical prognosis and tumor microenvironment (TME) of bladder cancer (BLCA) are insufficiently understood.

Method

BLCA patients were classified into different anoikis subtypes based on the expression of candidate anoikis-related genes (ARGs), and differences in the clinicopathological features, TME, immune cell infiltration, and immune checkpoints between two anoikis subtypes were analyzed. Next, patients in the TCGA cohort were randomized into the train and test groups in a 1:1 ratio. Subsequently, the anoikis-related model was constructed to predict the prognosis via utilizing the univariate Cox, LASSO and multivariate Cox analyses, and validated internally and externally. Moreover, the relationships between the risk score and clinicopathologic features, immune cell infiltration, immunotherapy response, and antitumor drug sensitivity were also analyzed. In addition, representative genes were evaluated using immunohistochemistry in clinical specimens, and in BLCA cell lines, functional experiments were performed to determine the biological behavior of hub gene PLOD1.

Result

Two definite anoikis subgroups were identified. Compared to ARGcluster A, patients assigned to ARGcluster B were characterized by an immunosuppressive microenvironment and worse prognosis. Then, the anoikis-related model, including PLOD1, EHBP1, and CSPG4, was constructed, and BLCA patients in the low-risk group were characterized by a better prognosis. Next, the accurate nomogram was built to improve the clinical applicability by combining the age, tumor stage and risk Score. Moreover, immune infiltration and clinical features differed significantly between high- and low-risk groups. We also found that the low-risk group exhibited a lower tumor immune dysfunction and exclusion score, a higher immunophenoscore (IPS), had more sensitivity to immunotherapy. Eventually, the expression levels of three genes were verified by our experiment, and knockdown of PLOD1 could inhibit invasion and migration abilities in BLCA cell lines.

Conclusion

These results demonstrated a new direction in precision therapy for BLCA, and indicated that the ARGs might be helpful to in predicting prognosis and as therapeutic targets in BLCA.

A novel prognostic model based on telomere-related lncRNAs in gastric cancer

Background

Telomeres are specialized structures at the ends of chromosomes that are important for their protection. Over time, long non-coding RNAs (lncRNAs) have gradually come into the spotlight as essential biomarkers of proliferation, migration, and invasion of human malignant tumors. Nevertheless, the impact of telomere-related lncRNAs (TRLs) in gastric cancer is currently unknown. In the present study, we screen the TRLs and identify a prognostic TRLs signature in gastric cancer.

Methods

First, telomere-related genes (TRGs) were retrieved from the website, and RNA sequencing (RNA-seq) data and clinical data of stomach adenocarcinoma (STAD) patients were gathered from The Cancer Genome Atlas (TCGA) database. Gastric cancer patients' lncRNAs and overall survival (OS) were found to be related using univariate Cox regression analysis. Next, least absolute shrinkage and selection operator (LASSO) regression analysis and multifactorial Cox regression analysis were used to further screen telomere-related differentially expressed lncRNAs (TRDELs), and finally six lncRNAs were obtained, including LINC01537, CFAP61-AS1, DIRC1, RABGAP1L-IT1, DBH-AS1, and REPIN1-AS1. According to these six TRDELs, a prognostic model for gastric cancer was constructed. The samples were divided into the training group and the testing group at random, and the reliability of prognostic model was validated in both groups and overall samples. In addition, we performed Kaplan-Meier (K-M) survival curve analysis, independent prognostic analysis, and functional enrichment analysis to validate the predictive value and independence of the model, as well as immune cell correlation analysis, clustering analysis, and principal component analysis (PCA) to further explore the relationship between this model and the tumor cells. Finally, we performed the drug sensitivity analysis to identify a few small molecules that may have a therapeutic effect on gastric cancer.

Results

Finally, we constructed a prognostic model for gastric cancer consisting of six TRDELs. According to the K-M curve, the prognosis of the low-risk group was noticeably superior than that of the high-risk group. Multivariate Cox regression analysis suggested that risk score was an independent prognostic element. Receiver operating characteristic (ROC) curves, nomogram, and calibration curve indicated that the prognostic model had good predictive ability. Functional enrichment analysis demonstrated major pathways with high- and low-risk groups. Next, both tumor microenvironment (TME) and immune correlation analysis showed discrepancy in the high- and low-risk groups. Through drug sensitivity analysis, we screened four small molecules that might be beneficial for gastric cancer treatment.

Conclusions

A prognostic model consisting of these six TRDELs was capable to predict the prognosis of gastric cancer patients.

Construction and Evaluation of an M2 Macrophage-Related Prognostic Model for Colon Cancer

Colon cancer (CC) is a primary human malignancy. Recently, the mechanism of the tumor microenvironment (TME) in CC has been a hot topic of research. However, there is uncertainty regarding the contribution of M2 macrophages and related genes to the prognosis for CC. M2 macrophage-related genes (M2RGs) were obtained from The Cancer Genome Atlas (TCGA) database. Immune cell infiltration in CC tissue was assessed by Cibersort. Based on the TCGA-COAD training set, a Least Absolute Shrinkage and Selection Operator (LASSO) Cox risk model was constructed and its efficiency was evaluated by analyzing risk profiles and survival profiles. Using gene set enrichment analysis (GSEA), the functional distinctions between high-risk and low-risk categories were further investigated. Finally, potential immune checkpoints, immunotherapy efficiency, and clinical treatment of high-risk patients were evaluated. A total of 1063 M2RGs were identified in TCGA-COAD, 32 of these were confirmed to be strongly related to overall survival (OS), and 14 of these were picked to construct an OS-oriented prognostic model in CC patients. The M2RG signature had a positive correlation with unfavorable prognosis according to the survival analysis. Correlation analysis revealed that the risk model was positively associated with clinicopathological characteristics, immune cell infiltration, immune checkpoint inhibitor targets, the risk of immune escape, and the efficiency of anti-cancer medications. The risk model created using M2RGs may be useful in predicting the prognosis of CC.

Identification of a novel cellular senescence-related lncRNA signature for prognosis and immune response in osteosarcoma

Background

Cellular senescence, a novel hallmark of cancer, is associated with patient outcomes and tumor immunotherapy. However, at present, there is no systematic study on the use of cellular senescence-related long non-coding RNAs (CSR-lncRNAs) to predict survival in patients with osteosarcoma. In this study, we aimed to identify a CSR-lncRNAs signature and to evaluate its potential use as a survival prognostic marker and predictive tool for immune response of osteosarcoma.

Methods

We downloaded a cohort of patients with osteosarcoma from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. We performed differential expression and co-expression analyses to identify CSR-lncRNAs. We performed univariate and multivariate Cox regression analyses along with the random forest algorithm to identify lncRNAs significantly correlated with senescence. Subsequently, we assessed the predictive models using survival curves, receiver operating characteristic curves, nomograms, C-index, and decision curve analysis. Based on this model, patients with osteosarcoma were divided into two groups according to their risk scores. Then, using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, we compared their clinical characteristics to uncover functional differences. We further conducted immune infiltration analyses using estimation of stromal and immune cells in malignant tumor tissues using expression data (ESTIMATE), cell-type identification by estimating relative subsets of rna transcripts (CIBERSORT), and single-sample gene set enrichment analysis for the two groups. We also evaluated the expression of the target genes of immune checkpoint inhibitors (ICIs).

Results

We identified six lncRNAs that were significantly correlated with senescence and accordingly established a novel cellular senescence-related lncRNA prognostic signature incorporating these lncRNAs. The nomogram indicated that the risk model was an independent prognostic factor that could predict the survival of patients with osteosarcoma. This model demonstrated high accuracy upon validation. Further analysis revealed that patients with osteosarcoma in the low-risk group exhibited better clinical outcomes and enhanced immune infiltration.

Conclusions

The six-CSR-lncRNA prognostic signature effectively predicted survival outcomes and patients in the low-risk group might have improved immune infiltration.

Prognostic value and potential function of a novel heme-related LncRNAs signature in gastric cancer

Heme is a coordination complex formed by the binding of iron ions and porphyrin rings. Its metabolic processes are associated with various cancers, including gastric cancer (GC). In recent years, long non-coding RNAs (LncRNAs) have been identified as key regulatory factors in GC. However, the role of LncRNAs associated with heme metabolism in GC and their relationship with prognosis have not been reported. In this study, we constructed a novel LncRNAs signature related to heme metabolism (HMlncSig) and validated its prognostic value for predicting the survival of GC patients through training, test, and entire cohorts. Kaplan-Meier analysis demonstrated that patients in the high-risk group had shorter survival times. Univariate and multivariate Cox regression analysis showed that HMlncSig was an independent prognostic indicator for GC patients, regardless of other clinical pathological features. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis and gene set variation analysis pathways showed that the activation of these markers may be involved in tumor progression, influencing the survival of GC patients. The nomogram, based on HMlncSig score and clinical features, demonstrated the strong predictive ability of this signature. Additionally, significant differences were observed between the high-risk and low-risk groups in terms of immune cell subtypes, expression of immune checkpoint genes, and response to chemotherapy and immunotherapy. Through clinical validation, we found that the risk score and heme levels of GC patients were both significantly elevated and correlated with the degree of malignancy. Furthermore, we found that AP000692.1, a key gene in this signature, promoted the proliferation, migration, and invasion of GC cells. In conclusion, our HMlncSig model has significant predictive value for the prognosis of GC patients and can provide clinical guidance for personalized immunotherapy.

Identification of a fatty acid metabolism-related gene signature to predict prognosis in stomach adenocarcinoma

BACKGROUND

Fatty acid metabolism (FAM) contributes to tumorigenesis and tumor development, but the role of FAM in the progression of stomach adenocarcinoma (STAD) has not been comprehensively clarified.

METHODS

The expression data and clinical follow-up information were obtained from The Cancer Genome Atlas (TCGA). FAM pathway was analyzed by gene set enrichment analysis (GSEA) and single-sample GSEA (ssGSEA) methods. Univariate Cox regression analysis was conducted to select prognosis genes. Molecular subtypes were classified by consensus clustering analysis. Furthermore, least absolute shrinkage and selection operator (Lasso) analysis was employed to develop a risk model. ESTIMATE and tumour immune dysfunction and exclusion (TIDE) algorithm were used to assess immunity. pRRophetic package was conducted to predict drug sensitivity.

RESULTS

Based on 14 FAM related prognosis genes (FAMRG), 2 clusters were determined. Patients in C2 showed a worse overall survival (OS). Furthermore, a 7-FAMRG risk model was established as an independent predictor for STAD, with a higher riskscore indicating an unfavorable OS. High riskscore patients had higher TIDE score and these patients were more sensitive to anticancer drugs such as Bortezomib, Dasatinib and Pazopanib. A nomogram based on riskscore was an effective prediction tool applicable to clinical settings. The results from pan-cancer analysis supported a prominent application value of riskscore model in other cancer types.

CONCLUSION

The FAMRGs model established in this study could help predict STAD prognosis and offer new directions for future studies on dysfunctional FAM-induced damage and anti-tumor drugs in STAD disease.

High expression of SRSF1 facilitates osteosarcoma progression and unveils its potential mechanisms

BACKGROUND

SRSF1, a member of Serine/Arginine-Rich Splicing Factors (SRSFs), has been observed to significantly influence cancer progression. However, the precise role of SRSF1 in osteosarcoma (OS) remains unclear. This study aims to investigate the functions of SRSF1 and its underlying mechanism in OS.

METHODS

SRSF1 expression level in OS was evaluated on the TCGA dataset, TAGET-OS database. qRT-PCR and Western blotting were employed to assess SRSF1 expression in human OS cell lines as well as the interfered ectopic expression states. The effect of SRSF1 on cell migration, invasion, proliferation, and apoptosis of OS cells were measured by transwell assay and flow cytometry. RNA sequence and bioinformatic analyses were conducted to elucidate the targeted genes, relevant biological pathways, and alternative splicing (AS) events regulated by SRSF1.

RESULTS

SRSF1 expression was consistently upregulated in both OS samples and OS cell lines. Diminishing SRSF1 resulted in reduced proliferation, migration, and invasion and increased apoptosis in OS cells while overexpressing SRSF1 led to enhanced growth, migration, invasion, and decreased apoptosis. Mechanistically, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and Gene Set Enrichment Analysis (GSEA) revealed that the biological functions of SRSF1 were closely associated with the dysregulation of the protein targeting processes, location of the cytosolic ribosome, extracellular matrix (ECM), and proteinaceous extracellular matrix, along with the PI3K-AKT pathway, Wnt pathway, and HIPPO pathway. Transcriptome analysis identified AS events modulated by SRSF1, especially (Skipped Exon) SE events and (Mutually exclusive Exons) MXE events, revealing potential roles of targeted molecules in mRNA surveillance, RNA degradation, and RNA transport during OS development. qRT-PCR confirmed that SRSF1 knockdown resulted in the occurrence of alternative splicing of SRRM2, DMKN, and SCAT1 in OS.

CONCLUSIONS

Our results highlight the oncogenic role of high SRSF1 expression in promoting OS progression, and further explore the potential mechanisms of action. The significant involvement of SRSF1 in OS development suggests its potential utility as a therapeutic target in OS.

The Impact of Long Noncoding RNAs in Tissue Regeneration and Senescence

Overcoming senescence with tissue engineering has a promising impact on multiple diseases. Here, we provide an overview of recent studies in which cellular senescence was inhibited through the up/downregulation of specific lncRNAs. This approach prevented senescence in the bones, joints, nervous system, heart, and blood vessels, with a potential impact on regeneration and the prevention of osteoarthritis and osteoporosis, as well as neurodegenerative and cardiovascular diseases. Senescence of the skin and liver could also be prevented through the regulation of cellular levels of specific lncRNAs, resulting in the rejuvenation of cells from these organs and their potential protection from disease. From these exciting achievements, which support tissue regeneration and are not restricted to stem cells, we propose lncRNA regulation through RNA or gene therapies as a prospective preventive and therapeutic approach against aging and multiple aging-related diseases.

Construction of stomach adenocarcinoma prognostic signature based on anoikis-related lncRNAs and clinical significance

As a dominant type of gastric cancer, stomach adenocarcinoma (STAD) is characterized by high morbidity and mortality rates. Anoikis factors participate in tumor metastasis and invasion. This study was designed to identify prognostic risk factors in anoikis-related long non-coding RNAs (lncRNAs) for STAD. First, with STAD expression datasets and anoikis-related gene sets downloaded from public databases, anoikis-related prognostic lncRNA signatures (AC091057.1, ADAMTS9.AS1, AC090825.1, AC084880.3, EMX2OS, HHIP.AS1, AC016583.2, EDIL3.DT, DIRC1, LINC01614, and AC103702.2) were screened by Cox regression to establish a prognostic risk model. Kaplan-Meier and receiver operating characteristic curves were used to evaluate the survival status of patients and verify predictive accuracy of the model. Besides, risk score could be an independent prognostic factor to assess the prognosis of STAD patients. Nomograms of the prognostic model that combined clinical information and risk score could effectively predict survival of STAD patients, as validated by calibration curve. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses were performed for differentially expressed genes (DEGs) in high- and low-risk groups. These DEGs were related to neurotransmitter transmission, signal transmission, and endocytosis. Moreover, we analyzed immune status of different risk groups and found that STAD patients in low-risk group were more sensitive to immunotherapy. A prognostic risk assessment model for STAD using anoikis-related lncRNA genes was constructed here, which was proven to have high predictive accuracy and thus could offer a reference for prognostic evaluation and clinical treatment of STAD patients.

Development of an immunogenic cell death prognostic signature for predicting clinical outcome and immune infiltration characterization in stomach adenocarcinoma

Stomach adenocarcinoma (STAD) is a common gastric histological cancer type with a high mortality rate. Immunogenic cell death (ICD) plays a key factor during carcinogenesis progress, whereas the prognostic value and role of ICD-related genes (ICDRGs) in STAD remain unclear. The MSigDB database collecting ICDRGs were selected by univariate Cox regression analysis and LASSO algorithm to establish a novel risk model. The Kaplan-Meier survival analysis indicated a significant difference of OS rate of patients by risk score stratification. ESTIMATE, CIBERSORT, and single sample gene set enrichment analysis (ssGSEA) algorithms were conducted to estimate the immune infiltration landscape by risk stratification. Subgroup analysis and tumor mutation burden analysis were also analyzed to identify characteristics between groups. Differences in therapeutic responsiveness to chemotherapeutic drugs and targeted drugs were also analyzed between high-risk group and low-risk group. The impact of one ICDRG, GPX1, on the proliferation, migration and invasiveness of was confirmed by in vitro experiments in GC cells to test the reliability of bioinformatics results. This study gives evidence of the involvement of ICD process in STAD and provides a new perspective for further accurate assessment of prognosis and therapeutic efficacy in STAD patients. Stomach adenocarcinoma (STAD) is a common gastric histological cancer type with a high mortality rate. Immunogenic cell death (ICD) plays a key factor during carcinogenesis progress, whereas the prognostic value and role of ICD-related genes (ICDRGs) in STAD remains unclear. The MSigDB database collected ICDRGs were selected by univariate Cox regression analysis and LASSO algorithm to establish a novel risk model. The Kaplan-Meier survival analysis indicated a significant difference of OS rate of patients by risk score stratification. ESTIMATE, CIBERSORT, and single sample gene set enrichment analysis (ssGSEA) algorithms were conducted to estimate the immune infiltration landscape by risk stratification. Subgroup analysis and tumor mutation burden analysis were also analyzed to identify characteristics between groups. Differences in therapeutic responsiveness to chemotherapeutic drugs and targeted drugs were also analyzed between high-risk group and low-risk group. The impact of one ICDRG, GPX1, on the proliferation, migration and invasiveness of was confirmed by in vitro experiments in GC cells to test the reliability of bioinformatics results. This study gives evidence of the involvement of ICD process in STAD and provides a new perspective for further accurate assessment of prognosis and therapeutic efficacy in STAD patients.

Cuproptosis-related lncRNA SNHG16 as a biomarker for the diagnosis and prognosis of head and neck squamous cell carcinoma

Background

We aim to investigate the potential value of cuproptosis-related lncRNA signaling in predicting clinical prognosis and immunotherapy and its relationship with drug sensitivity in head and neck squamous cell carcinoma (HNSCC).

Methods

We first identified the lncRNAs associated with cuproptosis genes in HNSCC and then conducted a series of analytical studies to investigate the expression and prognostic significance of these lncRNAs. Finally, we used RT-qPCR to validate our findings in a laryngeal squamous cell carcinoma cell line and 12 pairs of laryngeal squamous cell carcinoma and adjacent normal tissues.

Results

We identified 11 differentially expressed lncRNAs that were associated with cuproptosis genes in HNSCC and also served as prognostic markers for this cancer. Enrichment analysis revealed that these lncRNAs were related to immune-related functions that were suppressed in patients with oncogene mutations in the high-risk group. The patients with a high tumor mutation burden exhibited poor overall survival (OS). We used the tumor immune dysfunction and exclusion model to show that the patients in the high-risk group had great potential for immune evasion and less effective immunotherapy. We also identified several drugs that could be effective in treating HNSCC. Experimental validation showed that AC090587.1 and AC012184.3 exhibited differential expression between the TU686 and HBE cell lines, and SNHG16 showed differential expression among the TU686, TU212, and control HBE cells. Among the 12 pairs of cancer and adjacent tissues collected in the clinic, only SNHG16 showed differential expression. Targeted therapy against SNHG16 holds promise as a prospective novel strategy for the clinical management of HNSCC.

Senescence-Related lncRNA Signature Predicts Prognosis, Response to Immunotherapy and Chemotherapy in Skin Cutaneous Melanoma

Skin cutaneous melanoma (SKCM) is a highly malignant and aggressive cancer. Previous studies have shown that cellular senescence is a promising therapeutic strategy to limit melanoma cell progression. However, models to predict the prognosis of melanoma based on senescence-related lncRNAs and the efficacy of immune checkpoint therapy remain undefined. In this study, we developed a predictive signature consisting of four senescence-related lncRNAs (AC009495.2, U62317.1, AATBC, MIR205HG), and we then classified patients into high- and low-risk groups. GSEA (Gene set enrichment analysis) showed different activation of immune-related pathways in two groups. In addition, there were significant differences between the scores of tumor immune microenvironment, tumor burden mutation, immune checkpoint expression, and chemotherapeutic drug sensitivity between the two groups of patients. It provides new insights to guide more personalized treatment for patients with SKCM.

Immune cell death-related lncRNA signature as a predictive factor of clinical outcomes and immune checkpoints in gastric cancer

Background: Immune cell death (ICD) is a type of tumor cell death that has recently been shown to activate and regulate tumor immunity. However, the role of ICD-related long non-coding RNAs (lncRNAs) in gastric cancer remains to be clarified. Methods: We obtained 375 tumor samples from the Cancer Genome Atlas (TCGA) database and randomly assigned them to training and verification groups. LASSO and Cox regression analysis were utilized to identify ICD-related lncRNAs and establish a risk model. The changes in the immune microenvironment of the two groups were compared by examining the tumor-infiltrating immune cells. Results: We established a tumor signature based on nine ICD-related lncRNAs. In light of the receiver operating characteristic and Kaplan-Meier curves, the prognostic values of this risk model were verified. Multivariate regression analysis showed that the risk score was an independent risk factor for the prognosis of patients in both the training cohort (HR 2.52; 95% CI: 1.65-3.87) and validation cohort (HR 2.70; 95% CI: 1.54-4.8). A nomogram was developed to predict the 1-, 3-, and 5-year survival of patients with gastric cancer, and the signature was linked to high levels of immunological checkpoint expression (B7-H3, VSIR). Conclusions: An ICD-related lncRNA signature could predict the immune response and prognosis of patients with gastric cancer. This prognostic signature could be employed to independently monitor the efficacy of immunotherapy for gastric cancer patients.

Novel m7G-related lncRNA signature for predicting overall survival in patients with gastric cancer

Presenting with a poor prognosis, gastric cancer (GC) remains one of the leading causes of disease and death worldwide. Long non-coding RNAs (lncRNAs) regulate tumor formation and have been long used to predict tumor prognosis. N7-methylguanosine (m7G) is the most prevalent RNA modification. m7G-lncRNAs regulate GC onset and progression, but their precise mechanism in GC is unclear. The objective of this research was the development of a new m7G-related lncRNA signature as a biomarker for predicting GC survival rate and guiding treatment. The Cancer Genome Atlas database helped extract gene expression data and clinical information for GC. Pearson correlation analysis helped point out m7G-related lncRNAs. Univariate Cox analysis helped in identifying m7G-related lncRNA with predictive capability. The Lasso-Cox method helped point out seven lncRNAs for the purpose of establishing an m7G-related lncRNA prognostic signature (m7G-LPS), followed by the construction of a nomogram. Kaplan-Meier analysis, univariate and multivariate Cox regression analysis, calibration plot of the nomogram model, receiver operating characteristic curve and principal component analysis were utilized for the verification of the risk model's reliability. Furthermore, q-PCR helped verify the lncRNAs expression of m7G-LPS in-vitro. The study subjects were classified into high and low-risk groups based on the median value of the risk score. Gene enrichment analysis confirmed the constructed m7G-LPS' correlation with RNA transcription and translation and multiple immune-related pathways. Analysis of the clinicopathological features revealed more progressive features in the high-risk group. CIBERSORT analysis showed the involvement of m7G-LPS in immune cell infiltration. The risk score was correlated with immune checkpoint gene expression, immune cell and immune function score, immune cell infiltration, and chemotherapy drug sensitivity. Therefore, our study shows that m7G-LPS constructed using seven m7G-related lncRNAs can predict the survival time of GC patients and guide chemotherapy and immunotherapy regimens as biomarker.

LncRNA and its role in gastric cancer immunotherapy

Gastric cancer (GC) is a potential dominant disease in tumor immunotherapy checkpoint inhibitors, and adoptive cell therapy have brought great hope to GC patients. However, only some patients with GC can benefit from immunotherapy, and some patients develop drug resistance. More and more studies have shown that long non-coding RNAs (lncRNAs) may be important in GC immunotherapy's prognosis and drug resistance. Here, we summarize the differential expression of lncRNAs in GC and their impact on the curative effect of GC immunotherapy, discuss potential mechanisms of activity in GC immunotherapy resistance regulated by lncRNAs. This paper reviews the differential expression of lncRNA in GC and its effect on immunotherapy efficacy in GC. In terms of genomic stability, inhibitory immune checkpoint molecular expression, the cross-talk between lncRNA and immune-related characteristics of GC was summarized, including tumor mutation burden (TMB), microsatellite instability (MSI), and Programmed death 1 (PD-1). At the same time, this paper reviewed the mechanism of tumor-induced antigen presentation and upregulation of immunosuppressive factors, as well as the association between Fas system and lncRNA, immune microenvironment (TIME) and lncRNA, and summarized the functional role of lncRNA in tumor immune evasion and immunotherapy resistance.

Construction of anoikis-related lncRNAs risk model: Predicts prognosis and immunotherapy response for gastric adenocarcinoma patients

Background: Anoikis acts as a programmed cell death that is activated during carcinogenesis to remove undetected cells isolated from ECM. Further anoikis based risk stratification is expected to provide a deeper understanding of stomach adenocarcinoma (STAD) carcinogenesis. Methods: The information of STAD patients were acquired from TCGA dataset. Anoikis-related genes were obtained from the Molecular Signatures Database and Pearson correlation analysis was performed to identify the anoikis-related lncRNAs (ARLs). We performed machine learning algorithms, including Univariate Cox regression and Least Absolute Shrinkage and Selection Operator (Lasso) analyses on the ARLs to build the OS-score and OS-signature. Clinical subgroup analysis, tumor mutation burden (TMB) detection, drug susceptibility analysis, immune infiltration and pathway enrichment analysis were further performed to comprehensive explore the clinical significance. Results: We established a STAD prognostic model based on five ARLs and its prognostic value was verified. Survival analysis showed that the overall survival of high-risk score patients was significantly shorter than that of low-risk score patients. The column diagrams show satisfactory discrimination and calibration. The calibration curve verifies the good agreement between the prediction of the line graph and the actual observation. TIDE analysis and drug sensitivity analysis showed significant differences between different risk groups. Conclusion: The novel prognostic model based on anoikis-related lncRNAs we identified could be used for prognosis prediction and precise therapy in gastric adenocarcinoma.

Identification of TGF-β signaling-related molecular patterns, construction of a prognostic model, and prediction of immunotherapy response in gastric cancer

Background: TGF-β signaling pathway plays an essential role in tumor progression and immune responses. However, the link between TGF-β signaling pathway-related genes (TSRGs) and clinical prognosis, tumor microenvironment (TME), and immunotherapy in gastric cancer is unclear. Methods: Transcriptome data and related clinical data of gastric cancer were downloaded from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and 54 TSRGs were obtained from the Molecular Signatures Database (MSigDB). We systematically analyzed the expression profile characteristics of 54 TSRGs in 804 gastric cancer samples and examined the differences in prognosis, clinicopathological features, and TME among different molecular subtypes. Subsequently, TGF-β-related prognostic models were constructed using univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analysis to quantify the degree of risk in each patient. Patients were divided into two high- and low-risk groups based on the median risk score. Finally, sensitivity to immune checkpoint inhibitors (ICIs) and anti-tumor agents was assessed in patients in high- and low-risk groups. Results: We identified two distinct TGF-β subgroups. Compared to TGF-β cluster B, TGF-β cluster A exhibits an immunosuppressive microenvironment with a shorter overall survival (OS). Then, a novel TGF-β-associated prognostic model, including SRPX2, SGCE, DES, MMP7, and KRT17, was constructed, and the risk score was demonstrated as an independent prognostic factor for gastric cancer patients. Further studies showed that gastric cancer patients in the low-risk group, characterized by higher tumor mutation burden (TMB), the proportion of high microsatellite instability (MSI-H), immunophenoscore (IPS), and lower tumor immune dysfunction and exclusion (TIDE) score, had a better prognosis, and linked to higher response rate to immunotherapy. In addition, the risk score and anti-tumor drug sensitivity were strongly correlated. Conclusion: These findings highlight the importance of TSRGs, deepen the understanding of tumor immune microenvironment, and guide individualized immunotherapy for gastric cancer patients.